R/APE_write.dna.R

In pievos101/PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

# Copyright
# This function is from the APE package on CRAN !
# Emmanuel Paradis <Emmanuel.Paradis at ird.fr>

APE_write.dna <- function (x, file, format = "interleaved", append = FALSE, nbcol = 6, 
    colsep = " ", colw = 10, indent = NULL, blocksep = 1) 
{
    format <- match.arg(format, c("interleaved", "sequential", 
        "fasta"))
    phylip <- if (format %in% c("interleaved", "sequential")) 
        TRUE
    else FALSE
    if (inherits(x, "DNAbin")) 
        x <- as.character(x)
    aligned <- TRUE
    if (is.matrix(x)) {
        N <- dim(x)
        S <- N[2]
        N <- N[1]
        xx <- vector("list", N)
        for (i in 1:N) xx[[i]] <- x[i, ]
        names(xx) <- rownames(x)
        x <- xx
        rm(xx)
    }
    else {
        N <- length(x)
        S <- unique(unlist(lapply(x, length)))
        if (length(S) > 1) 
            aligned <- FALSE
    }
    if (is.null(names(x))) 
        names(x) <- as.character(1:N)
    if (is.null(indent)) 
        indent <- if (phylip) 
            10
        else 0
    if (is.numeric(indent)) 
        indent <- paste(rep(" ", indent), collapse = "")
    if (format == "interleaved") {
        blocksep <- paste(rep("\n", blocksep), collapse = "")
        if (nbcol < 0) 
            format <- "sequential"
    }
    zz <- if (append) 
        file(file, "a")
    else file(file, "w")
    on.exit(close(zz))
    if (phylip) {
        if (!aligned) 
            stop("sequences must have the same length for\n interleaved or sequential format.")
        cat(N, " ", S, "\n", sep = "", file = zz)
        if (nbcol < 0) {
            nb.block <- 1
            nbcol <- totalcol <- ceiling(S/colw)
        }
        else {
            nb.block <- ceiling(S/(colw * nbcol))
            totalcol <- ceiling(S/colw)
        }
        SEQ <- matrix("", N, totalcol)
        for (i in 1:N) {
            X <- paste(x[[i]], collapse = "")
            for (j in 1:totalcol) SEQ[i, j] <- substr(X, 1 + 
                (j - 1) * colw, colw + (j - 1) * colw)
        }
        max.nc <- max(nchar(names(x)))
        fmt <- paste("%-", max.nc + 1, "s", sep = "")
        names(x) <- sprintf(fmt, names(x))
    }
    switch(format, interleaved = {
        colsel <- if (nb.block == 1) 1:totalcol else 1:nbcol
        for (i in 1:N) {
            cat(names(x)[i], file = zz)
            cat(SEQ[i, colsel], sep = colsep, file = zz)
            cat("\n", file = zz)
        }
        if (nb.block > 1) {
            for (k in 2:nb.block) {
                cat(blocksep, file = zz)
                endcolsel <- if (k == nb.block) totalcol else nbcol + 
                  (k - 1) * nbcol
                for (i in 1:N) {
                  cat(indent, file = zz)
                  cat(SEQ[i, (1 + (k - 1) * nbcol):endcolsel], 
                    sep = colsep, file = zz)
                  cat("\n", file = zz)
                }
            }
        }
    }, sequential = {
        if (nb.block == 1) {
            for (i in 1:N) {
                cat(names(x)[i], file = zz)
                cat(SEQ[i, ], sep = colsep, file = zz)
                cat("\n", file = zz)
            }
        } else {
            for (i in 1:N) {
                cat(names(x)[i], file = zz)
                cat(SEQ[i, 1:nbcol], sep = colsep, file = zz)
                cat("\n", file = zz)
                for (k in 2:nb.block) {
                  endcolsel <- if (k == nb.block) totalcol else nbcol + 
                    (k - 1) * nbcol
                  cat(indent, file = zz)
                  cat(SEQ[i, (1 + (k - 1) * nbcol):endcolsel], 
                    sep = colsep, file = zz)
                  cat("\n", file = zz)
                }
            }
        }
    }, fasta = {
        for (i in 1:N) {
            cat(">", names(x)[i], file = zz, sep = "")
            cat("\n", file = zz)
            X <- paste(x[[i]], collapse = "")
            S <- length(x[[i]])
            totalcol <- ceiling(S/colw)
            if (nbcol < 0) nbcol <- totalcol
            nb.lines <- ceiling(totalcol/nbcol)
            SEQ <- character(totalcol)
            for (j in 1:totalcol) SEQ[j] <- substr(X, 1 + (j - 
                1) * colw, colw + (j - 1) * colw)
            for (k in 1:nb.lines) {
                endsel <- if (k == nb.lines) length(SEQ) else nbcol + 
                  (k - 1) * nbcol
                cat(indent, file = zz)
                cat(SEQ[(1 + (k - 1) * nbcol):endsel], sep = colsep, 
                  file = zz)
                cat("\n", file = zz)
            }
        }
    })
}